With the advances in the information and computing technologies, the ways the manufacturing enterprise systems are being managed are changing. More integration and adoption of the system perspective push further towards a more flattened enterprise. This, in addition to the varying levels of aggregation and details and the presence of the continuous and discrete types of behavior, created serious challenges for the use of the existing simulation tools for simulating the modern manufacturing enterprise system. The commonly used discrete event simulation (DES) techniques face difficulties in modeling such integrated systems due to increased model complexity, the lack of data at the aggregate management levels, and the unsuitability of DES to model the financial sectors of the enterprise. System dynamics (SD) has been effective in providing the needs of top management levels but unsuccessful in offering the needed granularity at the detailed operational levels of the manufacturing system. On the other hand the existing hybrid continuous-discrete tools are based on certain assumptions that do not fit the requirements of the common decision making situations in the business systems.